Is there a way to generate an armature from a collection of points/vertices?
I would do it this way, requiring Blender and Blender Add-On: Sverchok and/or maybe Animation Nodes (!).

Supposedly all this can be done using Python Script, but for artist, maybe Sverchok or AN Animation Nodes is A LOT easier.


You start with some kind of data of point cloud. In CSV or whatever. I supposed you have recorded the data for each frame. I will start with just a single frame, this will be for the Rest Bones.

Load the CSV data into Sverchok via Text In node. Right away here, I am turning the point cloud into group of edges, merge, and this will be for the Bones, via Skin Modifier.





Poly Edge -> Skin Modifier -> Create Armature -> Bones! Magic!



Here, sometimes you need to Clear Parent for the Bones.


Next, we simply pipe in the animation data into the Pose Bone, frame by frame using Animation Nodes or Sverchok. Here is Sverchok way:




So.... that's pretty much it the basic idea.